levinas / samtools Goto Github PK

- added "samtools sample" command, to sample reads from a SAM/BAM file at a given frequency.
- added "samtools qa" command, to compute the mean and median coverage, as well a histogram 
from 1 to N (defined by param) containing the number of bases covered a maximum of 1X, 2X...NX. 
Furthermore, "other" information is also available in the output file, namely:
    - Total number of reads
    - Total number of duplicates found and ignored (duplicates are "found" based on the sam flag 
    and are ignored in the counting of coverage)
    - Percentage of unmapped reads
    - Percentage of zero quality mappings
    - Number of proper paired reads (based on sam flag of proper pairs)
    - Percentage of proper pairs.e

- Check the write filehandle after opening for write.
- allow for user defined [lowercase] tags in header elements.
- allow the maximum memory for "samtools sort" to be specified with units.
- adjust for leading hard clip on colorspace reads.
- catches and reports an invalid BAM header, instead of segfaulting later on.
- fixes a small underflow/overflow bug in integer parsing.
- checks for a lowerbound in text entry box to avoid segfault in tview.